TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Bioconductor version: 3.24 · Package version: 1.51.0
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TFBSTools")Details
| Maintainer | Ge Tan <ge_tan@live.com> |
| Author | Ge Tan [aut, cre] |
| License | GPL-2 |
| URL | https://github.com/ge11232002/TFBSTools |
| Bug Reports | https://github.com/ge11232002/TFBSTools/issues |
| Downloads rank | 4231 |
| Source branch | devel |
| biocViews | Alignment, GeneRegulation, MotifAnnotation, MotifDiscovery, Software, Transcription |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TFBSTools_1.51.0.tar.gz |
| Windows binary (x86_64) | TFBSTools_1.51.0.zip |
| macOS binary (arm64) | TFBSTools_1.51.0.tgz |
| macOS binary (x86_64) | TFBSTools_1.51.0.tgz |
Dependencies
Depends: R (>= 3.2.2)
Imports: Biobase (>= 2.28), Biostrings (>= 2.36.4), pwalign, BiocGenerics (>= 0.14.0), BiocParallel (>= 1.2.21), BSgenome (>= 1.36.3), caTools (>= 1.17.1), DirichletMultinomial (>= 1.10.0), Seqinfo, GenomicRanges (>= 1.20.6), gtools (>= 3.5.0), grid, IRanges (>= 2.2.7), methods, DBI (>= 0.6), RSQLite (>= 1.0.0), rtracklayer (>= 1.28.10), seqLogo (>= 1.34.0), S4Vectors (>= 0.9.25), TFMPvalue (>= 0.0.5), XML (>= 3.98-1.3), XVector (>= 0.8.0), parallel
Suggests: BiocStyle (>= 1.7.7), JASPAR2014 (>= 1.4.0), knitr (>= 1.11), testthat, JASPAR2016 (>= 1.0.0), JASPAR2018 (>= 1.0.0), rmarkdown
Reverse dependencies
Imports Me (8): ATACseqTFEA, chromVAR, esATAC, MatrixRider, monaLisa, motifmatchr, motifStack, primirTSS
Suggests Me (11): CAGEWorkflow, enhancerHomologSearch, epiSeeker, GRaNIE, JASPAR2018, JASPAR2020, JASPAR2022, MAGAR, pageRank, Signac, universalmotif